Main tool : VADR
Additional tools:
- perl v5.34.0
- infernal v1.1.5
- ncbi-blast+ v2.15.0
- fasta v36.3.8h (the tool, not the file format)
- minimap2 2.26-r1175
Basic information on how to use this tool:
- executable:
v-annotate.pl - additional executable:
fasta-trim-terminal-ambigs.pl - help:
-h - version:
-v
VADR is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It has been mainly tested for analysis of Norovirus, Dengue, and SARS-CoV-2 virus sequences in preparation for submission to the GenBank database.
Included models:
- Flu version 1.6.3-2 (
-mkey flu)
Most of the VADR model files are located at /opt/vadr/vadr-models in the container filesystem and this path is stored in the globally accessible bash variable $VADRMODELDIR. For most applications, there is no need to specify v-annotate.pl --mdir /path/to/model/files since $VADRMODELDIR is set in the environment.
- Full documentation: https://github.com/ncbi/vadr/wiki
- Flu model documentation: https://github.com/ncbi/vadr/wiki/Influenza-annotation
- Flu model publication: https://doi.org/10.1093/database/baae091
# trim fasta file
fasta-trim-terminal-ambigs.pl input.consensus.fa > trimmed.fasta
# run v-annotate.pl using Flu models
v-annotate.pl --split --cpu 8 -r --atgonly --xnocomp --nomisc \
--alt_fail extrant5,extrant3 --mkey flu \
trimmed.fa \
flu-test-output